Introduction Pharyngeal Neisseria gonorrhoeae infections are mostly asymptomatic, yet sustain ongoing gonococcal transmission. We assessed the proportion of pharyngeal gonorrhea that spontaneously clears and identified determinants of clearance. Methods At the sexually transmitted infections clinic Amsterdam, at-risk women and men who have sex with men were routinely screened for pharyngeal N. gonorrhoeae using an RNA-based nucleic acid amplification test (NAAT; Aptima Combo 2). We retrospectively examined medical records of pharyngeal gonorrhea patients (January 2012–August 2015). We included patients who returned for antibiotic treatment and had a new sample taken for NAAT before treatment. Spontaneous clearance was defined as a negative NAAT result at the follow-up visit. Results During the study period, 1266 cases with a pharyngeal gonorrhea were not treated at the first consultation and returned for a follow-up visit. Median (interquartile range) time between the first consultation and follow-up was 10 (7–14) days. Spontaneous clearance was found in 139 cases (11.0%) and was associated with age at least 45 years (vs. 16–24 years; adjusted odds ratio, 2.02 [95% confidence interval, 1.09–3.75]) and with time from the first consultation to follow-up (adjusted odds ratio, 1.08 [1.06–1.10], per extra day). Conclusions Eleven percent of pharyngeal gonorrhea cases cleared spontaneously. Spontaneous clearance of pharyngeal gonorrhea was more often seen among older patients.